Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_013009467.1 DACET_RS00570 aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000025725.1:WP_013009467.1 Length = 374 Score = 245 bits (625), Expect = 2e-69 Identities = 135/373 (36%), Positives = 208/373 (55%), Gaps = 10/373 (2%) Query: 13 PFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPE 72 PF VMD+ +R GD ++ GQP V AL Q Y+ A GI Sbjct: 9 PFIVMDI----LQRANEIGDCIHFEVGQPDMAPSGGVLDGMREALDDGQFPYTPAKGIMP 64 Query: 73 LRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNIL 132 LR+ I+ Y++ + + V P+ V++T G+SG FL+A+ D G+++A PGYPCY+N Sbjct: 65 LREKISDFYKQYYRVQVSPERVMLTVGTSGAFLIAYSILVDIGEKLAFTDPGYPCYKNYS 124 Query: 133 SALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWC 192 LG + V IP G +T +Q TA MLAE + ++ V ++SP NPTG + E L + +C Sbjct: 125 YVLGIDPVMIPVGAETNYQMTAGMLAEHE-NVKAVQISSPCNPTGNLYGKENLLGLIEYC 183 Query: 193 DASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVL 252 + D+ ISDE+YHGLVY G + + A + S +A+V+N FSKY+ M G RLGW+++P L Sbjct: 184 KSKDIGFISDEIYHGLVYSGVKEHT-ALEFSDDAIVINGFSKYFCMPGARLGWMILPEKL 242 Query: 253 RRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDR 312 R + + N I P +SQI V AF + + A Y R L + L+ I Sbjct: 243 VRPAEVVMQNLFISAPTMSQIGCVHAFDYKFLEDYK---AEYEKRRDFLYNELKSIFKID 299 Query: 313 LAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSG 372 + P +GAFY++AD+S+++ D F +LL + +A+ PG+DF G ++R ++ Sbjct: 300 VVP-EGAFYIWADISEYSDDCYNFALELLENARIAVTPGVDFGRNNTGKYIRFAYTRNIE 358 Query: 373 DIEEALRRIGSWL 385 + E +RR+ +L Sbjct: 359 HMAEGIRRLKEYL 371 Lambda K H 0.321 0.136 0.416 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 386 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 388 Length of database: 374 Length adjustment: 30 Effective length of query: 358 Effective length of database: 344 Effective search space: 123152 Effective search space used: 123152 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory